Cosmetic issue: Help / usage text for kSNP4 references self as kSNP3.

[kissake]

When run with the command 'kSNP4 -h' (with -h not being a valid argument), the errors listed below occur, and then the usage statement is shown with the name of the program showing kSNP3 instead of kSNP4.

# kSNP4 -h
Error: Unrecognized argument (no valid argument: -h)
Error: Must specify -k, -outdir, and -in. At least one is missing.
Usage: kSNP3 -k <kmer length> -outdir <output directory> -in <input fasta file> [<optional arguments>...]

[barryghall]

Hi Jeremiiah, I think your message is VERY important. Your message suggests that we need to start a “to do” list for the kSNP4.1 release. There were a number of your comments for the User Guide to which I responded something like “not now. Perhaps in the next release”. Those should all be added to the “to do” list. My first candidate for the list is that we need to have a uniform way to display a help screen and that should apply to EVERY program that can be called directly by the user. Entering the option -h should in every case display the help. At this time some programs display help when no argument is entered. Bad. Not uniform. For kSNP4 entering kSNP4 -h should display this: Must specify -k, -outdir, and -in. Usage: kSNP4 -k <kmer length, an odd number >= 7> -outdir <output directory> -in <input file> [<optional arguments>…] Example: kSNP4 -in Eco.in -k 21 -outdir EcoRun1 For optional arguments see the kSNP4 User Guide Arguments may be entered in any order Notice that under Usage -in does not mention fasta. That is because the input file is not a fasta Just below Usage is an Example line. That is important because we cannot expect the user to know that <output directory> means “enter the name of the output directory here. We both know that convention, but we can’t expect the user to know it. The Example line is an explicit example that also serves to teach the meaning of what is on the Usage line. The next line is because we don’t intend for the help screen to be a substitute for the User Guide. The last line, which should be at the end of every help screen. Notice also that there is no mention of an error because -h is a legitimate argument. Notice that I changed kSNP3 to kSNP4. If, on the other hand, the user fails to enter one of the required arguments the Error screen will be displayed: Error: Must specify -k, -outdir, and -in. At least one is missing. Usage: kSNP4 -k <kmer length> -outdir <output directory> -in <input fasta file> [<optional arguments>...] Example: kSNP4 -in Eco.in -k 21 -outdir EcoRun1 For optional arguments see the kSNP4 User Guide Arguments may be entered in any order My second candidate for the list is that EVERY argument should include a flag, even if there is a single argument. The user should not have to remember which program command lines use a flag and which do not. I know that I have a hard time remembering which arguments MakekSNP4infile requires. Just being able to enter MakekSNP4infile -h would save me from having to go to the User Guide again, and again, and again. We need to keep in mind that most people won’t run kSNP4 or its utility programs very often and KNOWING that they can just enter -h to get a help screen will make our programs much more use friendly Let’s start building the to do list separately, then reconcile our lists every week or so. Barry Barry G. Hall Director, Bellingham Research Institute ***@***.*** http://www.bellinghamresearch.com <http://www.bellinghamresearch.com/>

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On Oct 27, 2022, at 4:02 PM, kissake ***@***.***> wrote: When run with the command 'kSNP4 -h' (with -h not being a valid argument), the errors listed below occur, and then the usage statement is shown with the name of the program showing kSNP3 instead of kSNP4. # kSNP4 -h Error: Unrecognized argument (no valid argument: -h) Error: Must specify -k, -outdir, and -in. At least one is missing. Usage: kSNP3 -k <kmer length> -outdir <output directory> -in <input fasta file> [<optional arguments>...] — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEEW7EQG754QEGZVVHLF4PDWFMCXDANCNFSM6AAAAAARQQ7TTI>. You are receiving this because you are subscribed to this thread.